Designing Bioinformatic Pipeline to work on the Single cell RNA sequencing data analysis

Question

[Yasemin]

Hi there,

I am a beginner learner in Bioinformatics with a little bit of experience in R and python. I do have a project as designing a sc-rna seq data analysis and visualization pipeline to have it in-house, and currently we are using GeneSpring to work on the dataset.

My questions is that considering me being at the beginner level and wanted to learn, gain and build an experience with this project to be able to later on work on the field of Bioinformatics:

1. Where should I start?
2. How designing a pipeline works?
3. What would be the recommendation of yours overall?

Thanks in advance!

Yas

Answer 1

[Ming Tommy Tang]

the pipeline is for pre-processing? it seems you want to write one for visualization.
The downstream analysis can be very flexible depending on what you want to do, or you need to do the same downstream analysis for many times then you can start writing a pipeline.

I usually use Snakemake for pipeline. You can also look into Nextflow.

[Yasemin]

Hi there, thank you for your response! I would like to have a pipeline for both pre-processing and visualization. For pre-processing what you would recommend?